superelastix/elastix repository overview

In order to run the elastix docker the following things have to be done:

• Pull the docker file docker pull superelastix/elastix:latest. (replace latest with the tagname you want to pull)
• assign or make an output directory where elastix can save the logfiles and other output: mkdir output
• give the directory where you stored the elastix files (parameter files, image files etc.) to docker: replace the part "$(pwd)"/elastix-data with the absolute path to this elastix directory in the command below.
• replace the parameter and image file names (including extension) in the command below.
• replace the tagname (latest here) with the docker file you want to use.
• run: docker run -u $UID:$GROUPS --mount type=bind,source="$(pwd)"/output,target=/out -v "$(pwd)"/elastix-data:/elastix/ superelastix/elastix:latest elastix -out /out/ -p /elastix/Parameters.txt -f /elastix/fixed_image.mha -m /elastix/moving_image.mha
• or for transformix run: docker run -u $UID:$GROUPS --mount type=bind,source="$(pwd)"/output,target=/out -v "$(pwd)"/elastix-data:/elastix/ superelastix/elastix:latest transformix -out /out/ -tp /elastix/TransformParameters.txt -in inputImage.mha